En savoir plus

Abstract

Plant organogenesis involves the establishment and the long-term maintenance of a stem cell niche within the meristem resulting in the indeterminate growth of roots and stems. In addition, plants have an incredible ability to regenerate their roots even after the stem cell niche has been removed (upon wounding for example). During this process, cells present around the wounding site will start to change their identities, divide and reform a fully functional root with a brand-new stem cell niche within several days. Yet, the mechanisms underlying this capacity of plant to fully regenerate are still poorly understood. Hence, we use single-cell RNA-seq profiling in a time course during root regeneration to track the different genetic programs and the dynamics of cellular reprograming.

We developed novel approach that combines topic modeling and machine learning to identify the specific cells undergoing regeneration and trace their reprogramming using our time lapse series.

In addition, we used a pharmacological approach to analyze the role of chromatin remodeling and cell cycle in the process of cell fate switching. We thereby identified that certain genes are primed and can be activated rapidly during regeneration while other require opening of new chromatin regions to be expressed, ending in the transition to a new, specialized cell type. We also identified a set of genes requiring mechanisms that typically work to shut chromatin accessibility, showing that the loss of previous identity is crucial for a full identity switch. The work provides clues about the different mechanisms that shut down an old cell identity and allow transition to a new one. In addition, our new machine learning tool can lead to the fast and easy identification of cryptic cell states during cellular changes like the signature of trans differentiation.

A short summary about the potential of single nuclei RNAseq vs single Cell RNAseq, on multiple plant species (Arabidopsis, Maize, Sorghum, Setaria).

A propos de l'intervenant :

Ancien doctorant de Guillaume Bécard et Jean-Philippe Combier, Bruno souhaite partager les dernières avancées sur le single cell RNA seq. Il poursuit des collaborations avec Jean-Malo Couzigou et Sandra Bensmihen sur un sujet similaire.

• Page de l'équipe de recherche >>>
• Contact mail >>>